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Vulnerability record · CVE-2026-31970 · published 18 March 2026

CVE-2026-31970: Htslib heap-based buffer overflow vulnerability

HHtslib · Htslib

HTSlib is a library for reading and writing bioinformatics file formats. GZI files are used to index block-compressed GZIP [BGZF] files. In the GZI loading function, `bgzf_index_load_hfile()`, it was possible to trigger an integer overflow, leading to an under- or zero-sized buffer being allocated to store the index. Sixteen zero bytes would then be written to this buffer, and, depending on the result of the overflow the rest of the file may also be loaded into the buffer as well. If the function did attempt to load the data, it would eventually fail due to not reading the expected number of records, and then try to free the overflowed heap buffer. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. The easiest work-around is to discard any `.gzi` index files from untrusted sources, and use the `bgzip -r` option to recreate them.

7.1 CVSS 4.0 High EPSS 0.64% · top 51.6% CWE-122 · Heap-based buffer overflowCWE-131 · CWE-131
7.1CVSS 4.0 base score
0.64%EPSS exploitation probability, 30 days
NoNot in CISA KEV
1Affected product versions listed by NVD
3References
17 Jun 2026Last modified by NVD

Description

HTSlib is a library for reading and writing bioinformatics file formats. GZI files are used to index block-compressed GZIP [BGZF] files. In the GZI loading function, `bgzf_index_load_hfile()`, it was possible to trigger an integer overflow, leading to an under- or zero-sized buffer being allocated to store the index. Sixteen zero bytes would then be written to this buffer, and, depending on the result of the overflow the rest of the file may also be loaded into the buffer as well. If the function did attempt to load the data, it would eventually fail due to not reading the expected number of records, and then try to free the overflowed heap buffer. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. The easiest work-around is to discard any `.gzi` index files from untrusted sources, and use the `bgzip -r` option to recreate them.

CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:

Affected products

1 vulnerable configurations from NVD's CPE data, grouped by vendor and product.

References

LinkTags
https://github.com/samtools/htslib/commit/6dd0d7d0e9e7e2e173a28969e624db8bc8bb5828 Patch
https://github.com/samtools/htslib/security/advisories/GHSA-p345-84hx-fq6q MitigationPatchVendor Advisory
http://www.openwall.com/lists/oss-security/2026/03/18/9 Mailing ListThird Party Advisory

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Related vulnerabilities

Same products first, then exploited flaws of the same weakness class.

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Source: NIST National Vulnerability Database (record CVE-2026-31970), CISA KEV, FIRST EPSS (scores of 2026-09-27). This page is refreshed as NVD updates the record.